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Decomposing spatial heterogeneity of cell trajectories with Paella

Hou, W.; Ji, Z.

2022-09-06 bioinformatics
10.1101/2022.09.05.506682 bioRxiv
Show abstract

Spatial transcriptomics provides a unique opportunity to study continuous biological processes in a spatial context. We developed Paella, a computational method to decompose a cell trajectory into multiple spatial sub-trajectories and identify genes with differential temporal patterns across spatial sub-trajectories. Applied to spatial transcriptomics datasets of cancer, Paella identified spatially varying genes associated with tumor progression, providing insights into the spatial heterogeneity of cancer development.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.